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- PDB-3lyp: Structure of stringent starvation protein A homolog from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 3lyp
TitleStructure of stringent starvation protein A homolog from Pseudomonas fluorescens
ComponentsStringent starvation protein A
KeywordsTRANSCRIPTION / structural genomics / GST-superfamily / sspA / Stringent starvation protein A homolog / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Stringent starvation protein A, N-terminal / Stringent starvation protein A, C-terminal / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 ...Stringent starvation protein A, N-terminal / Stringent starvation protein A, C-terminal / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Stringent starvation protein A
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Structure of stringent starvation protein A homolog from Pseudomonas fluorescens
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stringent starvation protein A
B: Stringent starvation protein A


Theoretical massNumber of molelcules
Total (without water)49,6702
Polymers49,6702
Non-polymers00
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-15 kcal/mol
Surface area18590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.591, 53.917, 54.496
Angle α, β, γ (deg.)85.280, 71.050, 66.710
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Stringent starvation protein A


Mass: 24834.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf-5 / ATCC BAA-477 / Gene: PFL_5077, sspA / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4K6H7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Imidazole pH 8.0, 0.4M Sodium Phosphate, 1.6M Potassium Phosphate, 0.2M Nacl, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 54196 / % possible obs: 95.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.073 / Χ2: 2.1 / Net I/σ(I): 17.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.633.20.20126501.026194
1.63-1.663.30.18826831.169195.7
1.66-1.693.30.17427211.252195.2
1.69-1.723.30.15326941.347196.4
1.72-1.763.30.14327581.545195.6
1.76-1.83.30.12627641.579196.2
1.8-1.853.30.11926991.813196.1
1.85-1.93.30.10627281.926195.7
1.9-1.953.30.09527582.135197.6
1.95-2.023.30.08727462.293196.7
2.02-2.093.20.07927792.466196.6
2.09-2.173.20.07227592.488197.3
2.17-2.273.20.07327512.549197.6
2.27-2.393.20.07327832.8197.6
2.39-2.543.20.0727622.77197.3
2.54-2.743.20.07127822.794197.6
2.74-3.013.20.06727722.68197.6
3.01-3.453.10.06427002.48195.7
3.45-4.3430.06524542.349185.9
4.34-503.20.07124532.687186.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YY7

1yy7


Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.195 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.881 / SU B: 3.088 / SU ML: 0.051 / SU R Cruickshank DPI: 0.093 / SU Rfree: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES RESIDUAL ONLY, UNCHARACTERIZED ELECTRON DENSITY OBSERVED BETWEEN SIDE-CHAINS OF THE RESIDUES ARG-103 AND TRP-108 (CHAIN A and B). ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES RESIDUAL ONLY, UNCHARACTERIZED ELECTRON DENSITY OBSERVED BETWEEN SIDE-CHAINS OF THE RESIDUES ARG-103 AND TRP-108 (CHAIN A and B). DENSITY SIMILAR TO PEPTIDE CONTAINING GLY-ASN/ASP OBSERVED NEAR RESIDUES 28-29 OF CHAIN B IS NOT MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2741 5.1 %RANDOM
Rwork0.183 ---
obs0.185 54182 95.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.12 Å2 / Biso mean: 14.447 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20.17 Å2-0.47 Å2
2---0.51 Å20.36 Å2
3---0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3152 0 0 217 3369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223371
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.9964607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4315418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3222.792154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12815581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.121536
X-RAY DIFFRACTIONr_chiral_restr0.1040.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0222608
X-RAY DIFFRACTIONr_mcbond_it1.5711.52075
X-RAY DIFFRACTIONr_mcangle_it2.5123392
X-RAY DIFFRACTIONr_scbond_it3.48431296
X-RAY DIFFRACTIONr_scangle_it5.5284.51215
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 182 -
Rwork0.219 3764 -
all-3946 -
obs--94.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.071-0.0389-0.15631.03380.04461.47290.0199-0.07670.05620.0250.0001-0.0449-0.0341-0.0048-0.02010.033-0.0112-0.01640.0214-0.0010.0149-4.3089.8588.812
21.06530.03160.24231.19910.10061.24660.01120.0348-0.0172-0.00630.01680.02390.06170.022-0.02810.03310.00120.00160.02550.00450.01433.106-10.734-7.913
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 207
2X-RAY DIFFRACTION2B9 - 207

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